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3D Architecture of Chromatin in Leukemia Affects Gene Expression

NEW YORK – In a study published Monday in Nature Genetics, a team led by researchers at New York University School of Medicine found that differences in three-dimensional architecture of chromatin can affect the expression of certain genes associated with leukemia.  This happens through changes to the integrity of topologically associating domains (TADs) and specific enhancer-promoter interactions.

The researchers specifically investigated the 3D chromatin architecture in T cell acute lymphoblastic leukemia (T-ALL) by examining the dynamic responses of this architecture in primary human leukemia specimens to pharmacological agents. Systematic integration of matched in situ Hi-C, RNA-seq, and CTCF ChIP-seq datasets revealed widespread differences in intra-TAD chromatin interactions and TAD boundary insulation in T-ALL and identified what they called a TAD "fusion" event associated with the absence of CTCF-mediated insulation, enabling direct interactions between the MYC promoter and a distal super-enhancer.

The researchers also found that small-molecule inhibitors targeting either oncogenic signal transduction or epigenetic regulation could alter specific 3D interactions found in leukemia.

"Our study is the first to show that the naturally looped structure of genetic material in blood cells is changing in T cell leukemia," the publication's co-lead author Palaniraja Thandapani, a postdoctoral fellow at NYU Langone Health and the Perlmutter Cancer Center, said in a statement. "With this in mind, the most effective treatment for this type of leukemia may be a combination of a drug that targets the disease's cancer-causing genetic mutations and another that counters any changes to chromosomal 3D structure."

Abrogation of CTCF binding or inversion of its orientation in boundary regions can change TAD structure and reconfigure enhancer-promoter interactions, leading to aberrant gene activation and developmental defects, the researchers said. Using T-ALL as a model, they investigated the potential reorganization of global chromatin architecture in primary T-ALL samples, T-ALL cell lines, and healthy peripheral T cells, identifying recurrent structural differences at TAD boundaries and significant alterations in intra-TAD chromatin interactions that mirrored differences in gene expression.

Both types of alterations influenced effectors of oncogenic NOTCH1 signaling. For example, they identified a recurrent TAD boundary change in T-ALL within the MYC locus, which facilitated long-range interactions of the MYC promoter with a previously characterized NOTCH-bound super-enhancer. Further, inhibition of NOTCH1 signaling using gamma-secretase inhibitors (γSI) reduced chromatin looping in several enhancer-promoter pairs that were sensitive to γSI treatment, suggesting a direct role for NOTCH1 in organizing chromatin architecture.

The researchers also found that loss of chromatin interactions between enhancer-promoter loops was associated with a reduction in acetylation at H3K27ac at the respective enhancer, but that a subset of enhancer-promoter loops, including the MYC-super-enhancer loop, retained their interactions with target promoters after γSI treatment, despite being bound by NOTCH1. In an analysis of this interaction, they found that CDK7 binding was enriched in γSI-insensitive chromatin contacts.

Subsequent pharmacological inhibition of CDK7 using the covalent inhibitor THZ1 significantly reduced MYC promoter contacts with the super-enhancer, underlining the complexity of the factors regulating 3D architecture, the researchers noted.

"Taken together, our findings provide deeper insight into how 3D chromatin architecture can affect the regulatory landscape of oncogenes in human leukemia and suggest that some of the changes can be inhibited by targeted drug treatments," the authors wrote. "Overall, our study underscores the need for further investigation of factors that maintain or rewire 3D chromosomal interactions, especially during cellular transformation, as they could be potential targets for small-molecule drug development."